Comparison of sample preparation methods for ChIP-chip assays

Henriette O'Geen, Charles M. Nicolet, Kim Blahnik, Roland Green, Peggy J. Farnham

Research output: Contribution to journalArticle

122 Citations (Scopus)

Abstract

A single chromatin immunoprecipitation (ChIP) sample does not provide enough DNA for hybridization to a genomic tiling array. A commonly used technique for amplifying the DNA obtained from ChIP assays is ligation-mediated PCR (LM-PCR). However, using this amplification method, we could not identify Oct4 binding sites on genomic tiling arrays representing 1% of the human genome (ENCODE arrays). In contrast, hybridization of a pool of 10 ChIP samples to the arrays produced reproducible binding patterns and low background signals. However, the pooling method would greatly increase the number of ChIP reactions needed to analyze the entire human genome. Therefore, we have adapted the GenomePlex® whole genome amplification (WGA) method for use in ChIP-chip assays; detailed ChIP and amplification protocols used for these analyses are provided as supplementary material. When applied to ENCODE arrays, the products prepared using this new method resulted in an Oct4 binding pattern similar to that from the pooled Oct4 ChIP samples. Importantly, the signal-to-noise ratio using the GenomePlex WGA method is superior to the LM-PCR amplification method.

Original languageEnglish (US)
Pages (from-to)577-580
Number of pages4
JournalBioTechniques
Volume41
Issue number5
DOIs
StatePublished - Nov 2006

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Chromatin Immunoprecipitation
Chromatin
Assays
Amplification
Genes
Human Genome
Ligation
Genome
Polymerase Chain Reaction
DNA
Signal-To-Noise Ratio
Signal to noise ratio
Binding Sites

ASJC Scopus subject areas

  • Clinical Biochemistry
  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

O'Geen, H., Nicolet, C. M., Blahnik, K., Green, R., & Farnham, P. J. (2006). Comparison of sample preparation methods for ChIP-chip assays. BioTechniques, 41(5), 577-580. https://doi.org/10.2144/000112268

Comparison of sample preparation methods for ChIP-chip assays. / O'Geen, Henriette; Nicolet, Charles M.; Blahnik, Kim; Green, Roland; Farnham, Peggy J.

In: BioTechniques, Vol. 41, No. 5, 11.2006, p. 577-580.

Research output: Contribution to journalArticle

O'Geen, H, Nicolet, CM, Blahnik, K, Green, R & Farnham, PJ 2006, 'Comparison of sample preparation methods for ChIP-chip assays', BioTechniques, vol. 41, no. 5, pp. 577-580. https://doi.org/10.2144/000112268
O'Geen H, Nicolet CM, Blahnik K, Green R, Farnham PJ. Comparison of sample preparation methods for ChIP-chip assays. BioTechniques. 2006 Nov;41(5):577-580. https://doi.org/10.2144/000112268
O'Geen, Henriette ; Nicolet, Charles M. ; Blahnik, Kim ; Green, Roland ; Farnham, Peggy J. / Comparison of sample preparation methods for ChIP-chip assays. In: BioTechniques. 2006 ; Vol. 41, No. 5. pp. 577-580.
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